Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi‐C mapping, whole‐genome Bisulfite Sequencing (BS‐Seq), long‐read isoform sequencing (Iso‐Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein‐coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)‐including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full‐length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family.

Glyptostrobus pensilis is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected and sequenced using double-digest restriction site-associated DNA (ddRAD-seq). A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. The genetic diversity in the populations was found to be low (H_o = 0.08630, H_e = 0.03475, π = 0.07239), with a high genetic differentiation coefficient (F_st). When K = 4, the coefficient of variation (CV) error value was minimized, suggesting that the 137 individuals could be divided into four groups, with frequent gene flow between them. Principal component analysis (PCA) divided the seven populations into two major categories based on their north–south geographic location. The clustering was consistent with those obtained from the PCA. The main reasons for the endangerment of G. pensilis are likely to be poor natural regeneration, human disturbances, and climatic factors. It is recommended that methods such as in situ conservation, ex situ conservation, and the establishment of germplasm banks be implemented to maintain the genetic diversity of G. pensilis populations.

Bamboo forest density is a factor that critically impacts the growth of moso bamboo, soil quality, and productivity. In this study, four bamboo forest density treatment groups were established under a long-term bamboo-stocking retention model, namely 1200 ± 100, 1800 ± 100, 2400 ± 100, and 3000 ± 100 plants·hm⁻², while a traditional management model focused on selective logging, with a bamboo forest density of 2100 ± 100 plants·hm⁻² (CK), serving as the control group. The study aimed to investigate the impact of bamboo forest density on bamboo shoots, roots, and soil, identify key influencing factors, and determine the optimal management density for this management model. Under the novel management model, bamboo shoot yield and number exhibited a unimodal response to stand density. At a density of 2400 plants·hm⁻², the bamboo shoot yield reached its highest value of 18,822 kg·hm⁻², with 7080 shoots·hm⁻². Under the density of 2400 plants·hm⁻², the specific root length, specific root surface area and total nitrogen, phosphorus and potassium contents of 0–1 mm fine roots were higher, and the contents of soil organic matter, total nitrogen, available phosphorus and available potassium were also better. Correlation analysis showed that the bamboo shoot yield and the number of shoots were closely related to soil quality (water content, organic matter, total nitrogen, available phosphorus and available potassium), and the effect of root total nitrogen content on shoot yield was particularly significant (the explanation rate was 75.7%). The comprehensive growth status assessment (D3 > D4 > D2 > CK > D1) showed that there were differences in the performance of different density treatment groups. This information could help bamboo farmers improve yield while protecting soil quality.

Chamaecyparis hodginsii with a naturally narrow-crowned form combines ornamental value, landscape greening functions, and timber production potential, maki